RosettaHoles2: a volumetric packing measure for protein structure refinement and validation.

We present an improved version of RosettaHoles, a methodology for quantitative and visual characterization of protein core packing. RosettaHoles2 features a packing measure more rapidly computable, accurate and physically transparent, as well as a new validation score intended for structures submitted to the Protein Data Bank. The differential packing measure is parameterized to maximize the gap between computationally generated and experimentally determined X-ray structures, and can be used in refinement of protein structure models. The parameters of the model provide insight into components missing in current force fields, and the validation score gives an upper bound on the X-ray resolution of Protein Data Bank structures; a crystal structure should have a validation score as good as or better than its resolution.